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0  structures 724  species 0  interactions 1444  sequences 3  architectures

Family: ABC2_membrane_5 (PF13346)

Summary: ABC-2 family transporter protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "ATP-binding domain of ABC transporters". More...

ATP-binding domain of ABC transporters Edit Wikipedia article

2hyd.gif
Multidrug ABC transporter SAV1866, closed state
Identifiers
Symbol ABC_tran
Pfam PF00005
InterPro IPR003439
PROSITE PDOC00185
SCOP 1b0u
SUPERFAMILY 1b0u
TCDB 3.A.1
OPM superfamily 17
OPM protein 2hyd

In molecular biology, ATP-binding domain of ABC transporters is a water-soluble domain of transmembrane ABC transporters.

ABC transporters belong to the ATP-Binding Cassette superfamily, which uses the hydrolysis of ATP to translocate a variety of compounds across biological membranes. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.

Biological function[edit]

ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain.

Amino acid sequence[edit]

The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attacking water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site.

3D structure[edit]

The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms.[1][2] ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis.

Human proteins containing this domain[edit]

ABCA1; ABCA10; ABCA12; ABCA13; ABCA2; ABCA3; ABCA4; ABCA5; ABCA6; ABCA7; ABCA8; ABCA9; ABCB1; ABCB10; ABCB11; ABCB4; ABCB5; ABCB6; ABCB7; ABCB8; ABCB9; ABCC1; ABCC10; ABCC11; ABCC12; ABCC2; ABCC3; ABCC4; ABCC5; ABCC6; ABCC8; ABCC9; ABCD1; ABCD2; ABCD3; ABCD4; ABCE1; ABCF1; ABCF2; ABCF3; ABCG1; ABCG2; ABCG4; ABCG5; ABCG8; CFTR; MRP3; TAP1; TAP2; TAPL;

References[edit]

  1. ^ Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH (December 1998). "Crystal structure of the ATP-binding subunit of an ABC transporter". Nature 396 (6712): 703–7. doi:10.1038/25393. PMID 9872322. 
  2. ^ Hollenstein K, Dawson RJ, Locher KP (August 2007). "Structure and mechanism of ABC transporter proteins". Curr. Opin. Struct. Biol. 17 (4): 412–8. doi:10.1016/j.sbi.2007.07.003. PMID 17723295. 
  • Rosteck Jr, P. R.; Reynolds, P. A.; Hershberger, C. L. (1991). "Homology between proteins controlling Streptomyces fradiae tylosin resistance and ATP-binding transport". Gene 102 (1): 27–32. PMID 1864505. 
  • Blight, M. A.; Holland, I. B. (1990). "Structure and function of haemolysin B,P-glycoprotein and other members of a novel family of membrane translocators". Molecular microbiology 4 (6): 873–880. PMID 1977073. 
  • Higgins, C. F.; Hyde, S. C.; Mimmack, M. M.; Gileadi, U.; Gill, D. R.; Gallagher, M. P. (1990). "Binding protein-dependent transport systems". Journal of bioenergetics and biomembranes 22 (4): 571–592. doi:10.1007/BF00762962. PMID 2229036. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

ABC-2 family transporter protein Provide feedback

This family is related to the ABC-2 membrane transporter family PF01061 [1].

Literature references

  1. Reizer J, Reizer A, Saier MH Jr; , Protein Sci 1992;1:1326-1332.: A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. PUBMED:1303751 EPMC:1303751


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025699

This family is related to the ABC-2 membrane transporter family [PUBMED:1303751].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan ABC-2 (CL0181), which contains the following 10 members:

ABC2_membrane ABC2_membrane_2 ABC2_membrane_3 ABC2_membrane_4 ABC2_membrane_5 ABC2_membrane_6 CcmB DUF3526 DUF3533 PDR_CDR

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(126)
Full
(1444)
Representative proteomes NCBI
(2276)
Meta
(340)
RP15
(67)
RP35
(117)
RP55
(132)
RP75
(151)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(126)
Full
(1444)
Representative proteomes NCBI
(2276)
Meta
(340)
RP15
(67)
RP35
(117)
RP55
(132)
RP75
(151)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(126)
Full
(1444)
Representative proteomes NCBI
(2276)
Meta
(340)
RP15
(67)
RP35
(117)
RP55
(132)
RP75
(151)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:C2CY30
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 126
Number in full: 1444
Average length of the domain: 201.80 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 90.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 206
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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